Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015000.1 Kokia drynarioides strain JFW-HI SEQ_130044, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 34803
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 250 characters in sequence are not A, C, G, or T
Found at i:4840 original size:26 final size:25
Alignment explanation
Indices: 4811--4860 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
4801 ATATAAATTA
4811 TAAAACAAAAAAAAGTAAGAAAGGAT
1 TAAAACAAAAAAAA-TAAGAAAGGAT
** *
4837 TAAATTAAAAAAAATGAGAAAGGA
1 TAAAACAAAAAAAATAAGAAAGGA
4861 CAGGGGTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.68, C:0.02, G:0.16, T:0.14
Consensus pattern (25 bp):
TAAAACAAAAAAAATAAGAAAGGAT
Found at i:5956 original size:24 final size:24
Alignment explanation
Indices: 5924--5980 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
5914 AAATCAAAAT
5924 GTGTATATATATATATATACATGC
1 GTGTATATATATATATATACATGC
5948 GTGTATATATATATATATACATGC
1 GTGTATATATATATATATACATGC
*
5972 GTATATATA
1 GTGTATATA
5981 AAAAATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.12, T:0.42
Consensus pattern (24 bp):
GTGTATATATATATATATACATGC
Found at i:7015 original size:38 final size:38
Alignment explanation
Indices: 6890--7017 Score: 103
Period size: 38 Copynumber: 3.3 Consensus size: 38
6880 TGAGATGATA
* * *
6890 GCTTCAATTTGCCCTTTGATTAAGGTAAAATATTGGAT
1 GCTTCAATCTGCACTATGATTAAGGTAAAATATTGGAT
* * * * ** * * * *
6928 GCTTCAATTTACCCTATAATCGAGATAAGAGATTGGTGT
1 GCTTCAATCTGCACTATGATTAAGGTAAAATATTGG-AT
* *
6967 GTCTTCAATCTGCATTCTGATTAAGGTAAAATATTGGAT
1 G-CTTCAATCTGCACTATGATTAAGGTAAAATATTGGAT
7006 GCTTCAATCTGC
1 GCTTCAATCTGC
7018 CCCAAAGATT
Statistics
Matches: 67, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
38 39 0.58
39 4 0.06
40 24 0.36
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.37
Consensus pattern (38 bp):
GCTTCAATCTGCACTATGATTAAGGTAAAATATTGGAT
Found at i:7077 original size:38 final size:38
Alignment explanation
Indices: 7035--7159 Score: 119
Period size: 38 Copynumber: 3.2 Consensus size: 38
7025 ATTGACGTGT
* *
7035 CTTCAATCTGCCTTCTAATTAAAGTAAATGATTGGATG
1 CTTCAATCTGCCTTCTGATTAAAGTAAAAGATTGGATG
* ** *
7073 CTTCAATCTG-CTCCATGATTGGAGTAAAAGA-TCGATGTG
1 CTTCAATCTGCCTTC-TGATTAAAGTAAAAGATTGGA--TG
* * *
7112 TCTTCAATCTACCTTCTGATTAAGGTAAAAGATTGAATG
1 -CTTCAATCTGCCTTCTGATTAAAGTAAAAGATTGGATG
7151 CTTCAATCT
1 CTTCAATCT
7160 ACCCCATGAT
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
37 6 0.09
38 31 0.46
39 4 0.06
40 22 0.32
41 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (38 bp):
CTTCAATCTGCCTTCTGATTAAAGTAAAAGATTGGATG
Found at i:7152 original size:78 final size:78
Alignment explanation
Indices: 7021--7169 Score: 217
Period size: 78 Copynumber: 1.9 Consensus size: 78
7011 AATCTGCCCC
* * * * * *
7021 AAAGATTGACGTGTCTTCAATCTGCCTTCTAATTAAAGTAAATGATTGGATGCTTCAATCTGCTC
1 AAAGATCGACGTGTCTTCAATCTACCTTCTAATTAAAGTAAAAGATTGAATGCTTCAATCTACCC
7086 CATGATTGGAGTA
66 CATGATTGGAGTA
* * *
7099 AAAGATCGATGTGTCTTCAATCTACCTTCTGATTAAGGTAAAAGATTGAATGCTTCAATCTACCC
1 AAAGATCGACGTGTCTTCAATCTACCTTCTAATTAAAGTAAAAGATTGAATGCTTCAATCTACCC
7164 CATGAT
66 CATGAT
7170 CGGGGTAAGA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 62 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (78 bp):
AAAGATCGACGTGTCTTCAATCTACCTTCTAATTAAAGTAAAAGATTGAATGCTTCAATCTACCC
CATGATTGGAGTA
Found at i:7177 original size:38 final size:38
Alignment explanation
Indices: 7058--7184 Score: 112
Period size: 38 Copynumber: 3.3 Consensus size: 38
7048 TCTAATTAAA
* * * * *
7058 GTAAATGATTGGATGCTTCAATCTGCTCCATGATTGGA
1 GTAAAAGATTGAATGCTTCAATCTACCCCATGATTGGG
* * * **
7096 GTAAAAGATCGATGTGTCTTCAATCTACCTTC-TGATTAAG
1 GTAAAAGATTGA-ATG-CTTCAATCTACC-CCATGATTGGG
*
7136 GTAAAAGATTGAATGCTTCAATCTACCCCATGATCGGG
1 GTAAAAGATTGAATGCTTCAATCTACCCCATGATTGGG
*
7174 GTAAGAGATTG
1 GTAAAAGATTG
7185 GCTGATAGCT
Statistics
Matches: 68, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
37 1 0.01
38 36 0.53
39 4 0.06
40 26 0.38
41 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (38 bp):
GTAAAAGATTGAATGCTTCAATCTACCCCATGATTGGG
Found at i:7594 original size:47 final size:47
Alignment explanation
Indices: 7497--7658 Score: 173
Period size: 47 Copynumber: 3.4 Consensus size: 47
7487 TTACGACTTT
* * * *
7497 AACCTTTCCCTTCATATCTCCATGGTACAAGAT-TCGCCGTTGCAGCCTC
1 AACCTTTCCCTTGATATCT--ATGGTTCTAGATCT-GCCTTTGCAGCCTC
*
7546 AACCTTTCCCTTGATATCTATGGTTCTAGATCTGCCTTTGCAGGCTC
1 AACCTTTCCCTTGATATCTATGGTTCTAGATCTGCCTTTGCAGCCTC
** * *
7593 AACCTTTCCCTTGATATCTATAATTCTAGATCCGCCTTTGCGGCCTC
1 AACCTTTCCCTTGATATCTATGGTTCTAGATCTGCCTTTGCAGCCTC
* * * *
7640 GATCTTTCCCATCATATCT
1 AACCTTTCCCTTGATATCT
7659 TCTAAGGTAC
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
47 79 0.81
48 1 0.01
49 18 0.18
ACGTcount: A:0.19, C:0.31, G:0.14, T:0.36
Consensus pattern (47 bp):
AACCTTTCCCTTGATATCTATGGTTCTAGATCTGCCTTTGCAGCCTC
Found at i:9851 original size:65 final size:65
Alignment explanation
Indices: 9747--9876 Score: 260
Period size: 65 Copynumber: 2.0 Consensus size: 65
9737 TTGCGTTTGA
9747 GTGTACTATGTTTTATGCGGTTTTCAAAGCAATACACTTGTTATCCCCTTTCTCCTTGATTAAGG
1 GTGTACTATGTTTTATGCGGTTTTCAAAGCAATACACTTGTTATCCCCTTTCTCCTTGATTAAGG
9812 GTGTACTATGTTTTATGCGGTTTTCAAAGCAATACACTTGTTATCCCCTTTCTCCTTGATTAAGG
1 GTGTACTATGTTTTATGCGGTTTTCAAAGCAATACACTTGTTATCCCCTTTCTCCTTGATTAAGG
9877 CTACAACCTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 65 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.42
Consensus pattern (65 bp):
GTGTACTATGTTTTATGCGGTTTTCAAAGCAATACACTTGTTATCCCCTTTCTCCTTGATTAAGG
Found at i:13910 original size:19 final size:21
Alignment explanation
Indices: 13888--13926 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
13878 TCTCTTATTT
13888 TTTTTTATTT-T-TAAATATG
1 TTTTTTATTTATATAAATATG
13907 TTTTTTATTTATATAAATAT
1 TTTTTTATTTATATAAATAT
13927 ATATATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTTTTATTTATATAAATATG
Found at i:34658 original size:4 final size:4
Alignment explanation
Indices: 34649--34734 Score: 68
Period size: 4 Copynumber: 21.2 Consensus size: 4
34639 AAATAAACGG
* * *
34649 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * * *
34699 G-AA GAAG GAGAG GAAA GAAA -TAA GAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
34735 GTAATGTGTT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
3 5 0.07
4 50 0.75
5 12 0.18
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:34671 original size:17 final size:17
Alignment explanation
Indices: 34649--34734 Score: 83
Period size: 17 Copynumber: 5.3 Consensus size: 17
34639 AAATAAACGG
34649 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
34666 GAAAGAAAGAAAGG-AA
1 GAAAGAAAGAAAGGAAA
* *
34682 GAAGGAGAGGAAA-GAAA
1 GAAAGA-AAGAAAGGAAA
* *
34699 G-AAGAAGGAGAGGAAA
1 GAAAGAAAGAAAGGAAA
*
34715 GAAA-TAAG-AAGGAAA
1 GAAAGAAAGAAAGGAAA
34730 GAAAG
1 GAAAG
34735 GTAATGTGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
15 15 0.26
16 18 0.32
17 24 0.42
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:34723 original size:23 final size:20
Alignment explanation
Indices: 34648--34727 Score: 99
Period size: 20 Copynumber: 3.9 Consensus size: 20
34638 CAAATAAACG
*
34648 GGAAAGAAAGAAAGGAAAGA-A
1 GGAAAGAAAG-AA-GAAGGAGA
*
34669 AGAAAGAAAGGAAGAAGGAGA
1 GGAAAGAAA-GAAGAAGGAGA
34690 GGAAAGAAAGAAGAAGGAGA
1 GGAAAGAAAGAAGAAGGAGA
*
34710 GGAAAGAAATAAGAAGGA
1 GGAAAGAAAGAAGAAGGA
34728 AAGAAAGGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
20 33 0.62
21 19 0.36
22 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.01
Consensus pattern (20 bp):
GGAAAGAAAGAAGAAGGAGA
Done.